Multiple sequence alignment - TraesCS5B01G148200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G148200 chr5B 100.000 4349 0 0 1 4349 276663782 276659434 0.000000e+00 8032.0
1 TraesCS5B01G148200 chr5D 95.130 3778 147 19 581 4349 229183617 229187366 0.000000e+00 5923.0
2 TraesCS5B01G148200 chr5D 89.706 408 35 5 114 519 292704196 292703794 8.340000e-142 514.0
3 TraesCS5B01G148200 chr5D 87.956 274 26 4 581 849 45488030 45488301 2.520000e-82 316.0
4 TraesCS5B01G148200 chr5D 95.192 104 5 0 3 106 334037731 334037628 9.680000e-37 165.0
5 TraesCS5B01G148200 chr5D 94.231 104 6 0 3 106 334039922 334039819 4.500000e-35 159.0
6 TraesCS5B01G148200 chr5A 96.277 2498 88 3 968 3465 327438492 327436000 0.000000e+00 4093.0
7 TraesCS5B01G148200 chr5A 90.817 893 54 17 3473 4349 327435823 327434943 0.000000e+00 1170.0
8 TraesCS5B01G148200 chr5A 88.448 277 28 2 581 853 354314276 354314000 9.020000e-87 331.0
9 TraesCS5B01G148200 chr5A 97.959 49 1 0 968 1016 327441384 327441336 7.750000e-13 86.1
10 TraesCS5B01G148200 chr5A 100.000 45 0 0 968 1012 327551125 327551081 2.790000e-12 84.2
11 TraesCS5B01G148200 chr2A 90.385 416 37 3 105 519 209097361 209096948 1.060000e-150 544.0
12 TraesCS5B01G148200 chr7B 90.168 417 37 3 105 519 287966414 287966000 1.380000e-149 540.0
13 TraesCS5B01G148200 chr7B 94.340 106 6 0 1 106 287966587 287966482 3.480000e-36 163.0
14 TraesCS5B01G148200 chr4D 90.120 415 38 2 105 518 343406613 343407025 1.780000e-148 536.0
15 TraesCS5B01G148200 chr4D 89.928 417 33 8 105 520 309903375 309902967 2.980000e-146 529.0
16 TraesCS5B01G148200 chr4D 96.226 106 4 0 1 106 309903548 309903443 1.610000e-39 174.0
17 TraesCS5B01G148200 chr7D 89.880 415 39 2 105 518 384050499 384050087 8.280000e-147 531.0
18 TraesCS5B01G148200 chr7D 89.074 421 38 8 105 523 50639526 50639940 2.320000e-142 516.0
19 TraesCS5B01G148200 chr7D 86.039 308 35 6 581 883 63446599 63446903 1.510000e-84 324.0
20 TraesCS5B01G148200 chr7D 97.170 106 3 0 1 106 50639353 50639458 3.460000e-41 180.0
21 TraesCS5B01G148200 chr7D 94.340 106 6 0 1 106 547273875 547273980 3.480000e-36 163.0
22 TraesCS5B01G148200 chr7A 89.157 415 41 4 105 518 721502224 721502635 8.340000e-142 514.0
23 TraesCS5B01G148200 chr7A 87.319 276 32 2 581 853 5170827 5170552 3.270000e-81 313.0
24 TraesCS5B01G148200 chr1D 88.995 418 41 5 106 521 420654168 420653754 3.000000e-141 512.0
25 TraesCS5B01G148200 chr1D 87.273 275 31 4 581 851 487951732 487951458 1.170000e-80 311.0
26 TraesCS5B01G148200 chrUn 87.912 273 29 2 581 849 332581824 332581552 7.020000e-83 318.0
27 TraesCS5B01G148200 chr3D 87.912 273 29 2 581 849 30415687 30415959 7.020000e-83 318.0
28 TraesCS5B01G148200 chr3A 87.912 273 29 2 581 849 43293486 43293758 7.020000e-83 318.0
29 TraesCS5B01G148200 chr3A 94.340 106 6 0 1 106 12023835 12023730 3.480000e-36 163.0
30 TraesCS5B01G148200 chr1A 94.340 106 6 0 1 106 384294555 384294660 3.480000e-36 163.0
31 TraesCS5B01G148200 chr1A 94.340 106 6 0 1 106 486583424 486583529 3.480000e-36 163.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G148200 chr5B 276659434 276663782 4348 True 8032.000000 8032 100.000000 1 4349 1 chr5B.!!$R1 4348
1 TraesCS5B01G148200 chr5D 229183617 229187366 3749 False 5923.000000 5923 95.130000 581 4349 1 chr5D.!!$F2 3768
2 TraesCS5B01G148200 chr5A 327434943 327441384 6441 True 1783.033333 4093 95.017667 968 4349 3 chr5A.!!$R3 3381
3 TraesCS5B01G148200 chr7B 287966000 287966587 587 True 351.500000 540 92.254000 1 519 2 chr7B.!!$R1 518
4 TraesCS5B01G148200 chr4D 309902967 309903548 581 True 351.500000 529 93.077000 1 520 2 chr4D.!!$R1 519
5 TraesCS5B01G148200 chr7D 50639353 50639940 587 False 348.000000 516 93.122000 1 523 2 chr7D.!!$F3 522

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
576 648 0.103208 GACCATAGTGGAGGTCGCAG 59.897 60.000 2.45 0.00 44.23 5.18 F
1221 3147 0.755698 CCTACTCCAGAAGCGGGCTA 60.756 60.000 0.00 0.00 0.00 3.93 F
1665 3591 1.755395 GGCCATGGCTCTGATGCAA 60.755 57.895 34.70 0.00 41.60 4.08 F
3228 5154 1.070445 GAGCAGTGATGGCGCCTAT 59.930 57.895 29.70 19.23 36.08 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 3552 0.105778 TCATCGCGCCATATCCACAA 59.894 50.000 0.00 0.0 0.00 3.33 R
2757 4683 1.072159 AAAAGCACTCTCCGCAGCT 59.928 52.632 0.00 0.0 39.37 4.24 R
3290 5216 0.617935 TTGATTCTCGGCCATCACCA 59.382 50.000 2.24 0.0 0.00 4.17 R
4099 6234 0.606401 ACAGCGCAACCTAATGCAGT 60.606 50.000 11.47 0.0 46.76 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.806542 GTCCTTGACGTTGTGATGCAT 59.193 47.619 0.00 0.00 0.00 3.96
173 243 8.862325 AACTTGTGATGGTCAATTAATAGTGA 57.138 30.769 0.00 0.00 0.00 3.41
256 326 7.519032 TTTTGTTTTGGAAGGTTATCGAGAT 57.481 32.000 0.00 0.00 0.00 2.75
362 432 2.358957 TGGAATGAATCAGAACCTGCG 58.641 47.619 0.00 0.00 0.00 5.18
452 523 4.971282 AGTTGGTGAGAATGATGGGAGATA 59.029 41.667 0.00 0.00 0.00 1.98
467 538 7.929245 TGATGGGAGATAACGAATAAAAATCGA 59.071 33.333 2.65 0.00 42.76 3.59
527 599 8.678199 TCATTAGGAGTAGAGATTATGTATGCG 58.322 37.037 0.00 0.00 0.00 4.73
528 600 5.906113 AGGAGTAGAGATTATGTATGCGG 57.094 43.478 0.00 0.00 0.00 5.69
529 601 5.571285 AGGAGTAGAGATTATGTATGCGGA 58.429 41.667 0.00 0.00 0.00 5.54
531 603 5.416326 GGAGTAGAGATTATGTATGCGGACT 59.584 44.000 0.00 0.00 0.00 3.85
532 604 6.071840 GGAGTAGAGATTATGTATGCGGACTT 60.072 42.308 0.00 0.00 0.00 3.01
533 605 6.682746 AGTAGAGATTATGTATGCGGACTTG 58.317 40.000 0.00 0.00 0.00 3.16
536 608 6.162079 AGAGATTATGTATGCGGACTTGATG 58.838 40.000 0.00 0.00 0.00 3.07
537 609 6.015095 AGAGATTATGTATGCGGACTTGATGA 60.015 38.462 0.00 0.00 0.00 2.92
538 610 6.705302 AGATTATGTATGCGGACTTGATGAT 58.295 36.000 0.00 0.00 0.00 2.45
540 612 6.785488 TTATGTATGCGGACTTGATGATTC 57.215 37.500 0.00 0.00 0.00 2.52
541 613 3.123050 TGTATGCGGACTTGATGATTCG 58.877 45.455 0.00 0.00 0.00 3.34
543 615 1.358877 TGCGGACTTGATGATTCGTG 58.641 50.000 0.00 0.00 0.00 4.35
544 616 0.652592 GCGGACTTGATGATTCGTGG 59.347 55.000 0.00 0.00 0.00 4.94
546 618 2.346803 CGGACTTGATGATTCGTGGTT 58.653 47.619 0.00 0.00 0.00 3.67
548 620 2.420022 GGACTTGATGATTCGTGGTTGG 59.580 50.000 0.00 0.00 0.00 3.77
551 623 4.647611 ACTTGATGATTCGTGGTTGGTTA 58.352 39.130 0.00 0.00 0.00 2.85
552 624 5.067273 ACTTGATGATTCGTGGTTGGTTAA 58.933 37.500 0.00 0.00 0.00 2.01
553 625 5.181245 ACTTGATGATTCGTGGTTGGTTAAG 59.819 40.000 0.00 0.00 0.00 1.85
554 626 4.006989 TGATGATTCGTGGTTGGTTAAGG 58.993 43.478 0.00 0.00 0.00 2.69
555 627 2.156098 TGATTCGTGGTTGGTTAAGGC 58.844 47.619 0.00 0.00 0.00 4.35
556 628 2.224670 TGATTCGTGGTTGGTTAAGGCT 60.225 45.455 0.00 0.00 0.00 4.58
557 629 1.600023 TTCGTGGTTGGTTAAGGCTG 58.400 50.000 0.00 0.00 0.00 4.85
559 631 0.872388 CGTGGTTGGTTAAGGCTGAC 59.128 55.000 0.00 0.00 0.00 3.51
560 632 1.244816 GTGGTTGGTTAAGGCTGACC 58.755 55.000 12.16 12.16 36.45 4.02
561 633 0.847373 TGGTTGGTTAAGGCTGACCA 59.153 50.000 16.53 16.53 43.87 4.02
563 635 2.645297 TGGTTGGTTAAGGCTGACCATA 59.355 45.455 19.91 10.74 44.83 2.74
564 636 3.279434 GGTTGGTTAAGGCTGACCATAG 58.721 50.000 19.91 0.00 44.83 2.23
566 638 3.627395 TGGTTAAGGCTGACCATAGTG 57.373 47.619 16.53 0.00 40.85 2.74
567 639 2.238646 TGGTTAAGGCTGACCATAGTGG 59.761 50.000 16.53 0.00 40.85 4.00
570 642 1.207791 AAGGCTGACCATAGTGGAGG 58.792 55.000 2.45 0.00 40.96 4.30
575 647 2.199117 GACCATAGTGGAGGTCGCA 58.801 57.895 2.45 0.00 44.23 5.10
576 648 0.103208 GACCATAGTGGAGGTCGCAG 59.897 60.000 2.45 0.00 44.23 5.18
577 649 1.227380 CCATAGTGGAGGTCGCAGC 60.227 63.158 0.00 0.00 40.96 5.25
578 650 1.227380 CATAGTGGAGGTCGCAGCC 60.227 63.158 0.00 0.00 0.00 4.85
579 651 2.786495 ATAGTGGAGGTCGCAGCCG 61.786 63.158 0.00 0.00 0.00 5.52
617 690 4.080015 TCCGGTCAAACCCTAAATCATCAT 60.080 41.667 0.00 0.00 33.75 2.45
623 696 9.739276 GGTCAAACCCTAAATCATCATATATCA 57.261 33.333 0.00 0.00 30.04 2.15
667 740 5.418840 AGTGTATTTGACATGTTTCATCCCC 59.581 40.000 0.00 0.00 41.14 4.81
668 741 5.184864 GTGTATTTGACATGTTTCATCCCCA 59.815 40.000 0.00 0.00 41.14 4.96
669 742 4.806640 ATTTGACATGTTTCATCCCCAC 57.193 40.909 0.00 0.00 0.00 4.61
670 743 2.967745 TGACATGTTTCATCCCCACA 57.032 45.000 0.00 0.00 0.00 4.17
672 745 3.777087 TGACATGTTTCATCCCCACATT 58.223 40.909 0.00 0.00 0.00 2.71
673 746 4.158786 TGACATGTTTCATCCCCACATTT 58.841 39.130 0.00 0.00 0.00 2.32
744 817 1.526315 TCCCTACCTAGTGGATCGGA 58.474 55.000 0.00 0.00 37.04 4.55
753 826 7.614583 CCTACCTAGTGGATCGGAGATAAATAA 59.385 40.741 0.00 0.00 37.96 1.40
777 853 7.703058 AAGATATAAAGTTGGGTGAAGGTTG 57.297 36.000 0.00 0.00 0.00 3.77
828 904 1.623311 CCCACCAATCCCCTCAAAAAC 59.377 52.381 0.00 0.00 0.00 2.43
841 917 5.773176 CCCCTCAAAAACACTAGTACCAAAT 59.227 40.000 0.00 0.00 0.00 2.32
846 922 7.878036 TCAAAAACACTAGTACCAAATAAGGC 58.122 34.615 0.00 0.00 0.00 4.35
862 938 7.759433 CCAAATAAGGCCTAATGTGTGTTAAAG 59.241 37.037 5.16 0.00 0.00 1.85
867 943 4.081697 GGCCTAATGTGTGTTAAAGGCATT 60.082 41.667 12.76 6.87 42.44 3.56
868 944 5.102313 GCCTAATGTGTGTTAAAGGCATTC 58.898 41.667 6.30 0.00 40.57 2.67
954 1034 4.916983 TTTCACTTGAACAATCTGTGGG 57.083 40.909 0.00 0.00 34.14 4.61
964 1044 5.242838 TGAACAATCTGTGGGGTATTTGTTC 59.757 40.000 15.67 15.67 34.38 3.18
965 1045 4.086457 ACAATCTGTGGGGTATTTGTTCC 58.914 43.478 0.00 0.00 0.00 3.62
966 1046 2.483014 TCTGTGGGGTATTTGTTCCG 57.517 50.000 0.00 0.00 0.00 4.30
968 1048 2.027561 TCTGTGGGGTATTTGTTCCGAG 60.028 50.000 0.00 0.00 0.00 4.63
1080 3006 2.529389 AAGTCGCCTGACCCCCTT 60.529 61.111 0.00 0.00 46.74 3.95
1123 3049 4.787280 CCTCCCGCTCCTCCAGGT 62.787 72.222 0.00 0.00 36.34 4.00
1133 3059 4.778415 CTCCAGGTCACCGTCGCG 62.778 72.222 0.00 0.00 0.00 5.87
1221 3147 0.755698 CCTACTCCAGAAGCGGGCTA 60.756 60.000 0.00 0.00 0.00 3.93
1228 3154 3.145551 GAAGCGGGCTACTCGGGA 61.146 66.667 0.00 0.00 0.00 5.14
1364 3290 2.267324 GCTGAGGAGCGGCTTCTT 59.733 61.111 13.04 0.00 45.70 2.52
1383 3309 1.906990 TCCCGAACGAGTTCTCTCTT 58.093 50.000 13.27 0.00 38.45 2.85
1419 3345 4.148825 GCCTGTGATCGGTCCGCT 62.149 66.667 6.34 0.00 0.00 5.52
1448 3374 3.042560 GCTCCAGTTTGGCGCTTT 58.957 55.556 7.64 0.00 44.42 3.51
1534 3460 2.353357 CATGTATGCCAGACATGGGT 57.647 50.000 21.73 0.00 46.88 4.51
1611 3537 3.665675 GAACGCGATGCTGGAGGGT 62.666 63.158 15.93 0.00 0.00 4.34
1626 3552 2.509964 GGAGGGTTATGTCTCCAATGGT 59.490 50.000 0.00 0.00 46.54 3.55
1665 3591 1.755395 GGCCATGGCTCTGATGCAA 60.755 57.895 34.70 0.00 41.60 4.08
1735 3661 2.124695 GTTCCATCACGGGGGAGC 60.125 66.667 0.00 0.00 34.02 4.70
1809 3735 2.700371 TGATACCTCCGTGATGAATGCT 59.300 45.455 0.00 0.00 0.00 3.79
1815 3741 3.005554 CTCCGTGATGAATGCTCTTGTT 58.994 45.455 0.00 0.00 0.00 2.83
1941 3867 2.660715 GCATGATGAAGACGATAGAGCG 59.339 50.000 0.00 0.00 41.38 5.03
2088 4014 3.510531 TCCTATCGTCATGGCTACTCT 57.489 47.619 0.00 0.00 0.00 3.24
2103 4029 3.854809 GCTACTCTGACGATGTTCTTGTC 59.145 47.826 0.00 0.00 38.58 3.18
2145 4071 4.832248 TGCTTTCGAGATGTGGATTACTT 58.168 39.130 0.00 0.00 0.00 2.24
2196 4122 5.066375 CCTCAAGTTCAGAAACATTGTGACA 59.934 40.000 0.00 0.00 37.88 3.58
2310 4236 4.125703 CAGATGAGTTCACCTATTCAGCC 58.874 47.826 0.00 0.00 0.00 4.85
2311 4237 3.776969 AGATGAGTTCACCTATTCAGCCA 59.223 43.478 0.00 0.00 0.00 4.75
2327 4253 2.036217 CAGCCATTTTGTCTGCTTTCCA 59.964 45.455 0.00 0.00 30.08 3.53
2385 4311 5.292589 CCATGCAATTATTCTGAAACAAGGC 59.707 40.000 0.00 1.82 0.00 4.35
2425 4351 4.051237 CGTGTCAACTTCACTGATCAAGA 58.949 43.478 0.00 0.00 34.14 3.02
2453 4379 2.816087 CAGTGTTTGGATCAGTTCAGGG 59.184 50.000 0.00 0.00 0.00 4.45
2604 4530 3.243068 GCATGAACAAACCTGACGAGTTT 60.243 43.478 0.00 0.00 37.93 2.66
2695 4621 2.847234 TTGTCAGGACGGGGCACT 60.847 61.111 0.00 0.00 0.00 4.40
2757 4683 1.737236 GCAAAGTGCGGTGACATATCA 59.263 47.619 0.00 0.00 31.71 2.15
3093 5019 3.470267 GCGAAAGGCGTGATCGAA 58.530 55.556 16.20 0.00 43.41 3.71
3228 5154 1.070445 GAGCAGTGATGGCGCCTAT 59.930 57.895 29.70 19.23 36.08 2.57
3290 5216 2.468301 TCTGCAGAAGAGGCTAGGAT 57.532 50.000 15.67 0.00 0.00 3.24
3363 5289 5.046159 TGAGGTTTAGGGGTGTTGTGTATAG 60.046 44.000 0.00 0.00 0.00 1.31
3394 5320 4.688021 AGCACTAACAGCAGAATAGCTAC 58.312 43.478 0.00 0.00 44.54 3.58
3399 5325 3.810310 ACAGCAGAATAGCTACTGTCC 57.190 47.619 11.73 0.00 45.99 4.02
3519 5614 5.009410 AGTCAGGCATGCTGCTATTTATTTC 59.991 40.000 18.92 0.00 44.28 2.17
3552 5647 2.151202 GACAACGCTCCAATTGAAGGA 58.849 47.619 7.12 0.00 0.00 3.36
3565 5660 6.889177 TCCAATTGAAGGAATAACATGTGCTA 59.111 34.615 7.12 0.00 30.71 3.49
3566 5661 7.395772 TCCAATTGAAGGAATAACATGTGCTAA 59.604 33.333 7.12 0.00 30.71 3.09
3567 5662 8.199449 CCAATTGAAGGAATAACATGTGCTAAT 58.801 33.333 7.12 0.00 0.00 1.73
3571 5666 8.800370 TGAAGGAATAACATGTGCTAATAACA 57.200 30.769 0.00 0.00 0.00 2.41
3572 5667 9.237187 TGAAGGAATAACATGTGCTAATAACAA 57.763 29.630 0.00 0.00 0.00 2.83
3574 5669 9.855021 AAGGAATAACATGTGCTAATAACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
3575 5670 9.019656 AGGAATAACATGTGCTAATAACAAACA 57.980 29.630 0.00 0.00 0.00 2.83
3576 5671 9.072294 GGAATAACATGTGCTAATAACAAACAC 57.928 33.333 0.00 0.00 0.00 3.32
3577 5672 8.980143 AATAACATGTGCTAATAACAAACACC 57.020 30.769 0.00 0.00 0.00 4.16
3578 5673 5.041951 ACATGTGCTAATAACAAACACCG 57.958 39.130 0.00 0.00 0.00 4.94
3579 5674 4.757657 ACATGTGCTAATAACAAACACCGA 59.242 37.500 0.00 0.00 0.00 4.69
3580 5675 4.735662 TGTGCTAATAACAAACACCGAC 57.264 40.909 0.00 0.00 0.00 4.79
3581 5676 4.382291 TGTGCTAATAACAAACACCGACT 58.618 39.130 0.00 0.00 0.00 4.18
3582 5677 5.539979 TGTGCTAATAACAAACACCGACTA 58.460 37.500 0.00 0.00 0.00 2.59
3583 5678 6.167685 TGTGCTAATAACAAACACCGACTAT 58.832 36.000 0.00 0.00 0.00 2.12
3584 5679 6.651643 TGTGCTAATAACAAACACCGACTATT 59.348 34.615 0.00 0.00 0.00 1.73
3585 5680 7.818446 TGTGCTAATAACAAACACCGACTATTA 59.182 33.333 0.00 0.00 0.00 0.98
3586 5681 8.658609 GTGCTAATAACAAACACCGACTATTAA 58.341 33.333 0.00 0.00 0.00 1.40
3587 5682 9.386010 TGCTAATAACAAACACCGACTATTAAT 57.614 29.630 0.00 0.00 0.00 1.40
3643 5749 8.969260 ATAGTTCATTGATCAGATAAGCAACA 57.031 30.769 0.00 0.00 0.00 3.33
3707 5840 2.073716 TGGACCACCAACCGACCTT 61.074 57.895 0.00 0.00 43.91 3.50
3994 6129 1.228675 CTGGGTTCCTTTGGCTGCT 60.229 57.895 0.00 0.00 0.00 4.24
3996 6131 1.531602 GGGTTCCTTTGGCTGCTGT 60.532 57.895 0.00 0.00 0.00 4.40
4077 6212 1.669779 GATGCTGCATTCCTCAGTGAC 59.330 52.381 17.36 0.00 34.21 3.67
4078 6213 0.689055 TGCTGCATTCCTCAGTGACT 59.311 50.000 0.00 0.00 34.21 3.41
4079 6214 1.338484 TGCTGCATTCCTCAGTGACTC 60.338 52.381 0.00 0.00 34.21 3.36
4099 6234 9.817809 GTGACTCCTCATTTATATTTGTAGTCA 57.182 33.333 0.00 0.00 37.78 3.41
4286 6421 3.645687 GCTCCCACTCTTCTATCTTCCAT 59.354 47.826 0.00 0.00 0.00 3.41
4296 6431 5.485353 TCTTCTATCTTCCATGTGAGGTTGT 59.515 40.000 0.00 0.00 0.00 3.32
4310 6445 1.364901 GTTGTGGCATTGCAGTGCT 59.635 52.632 29.95 0.00 44.45 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 3.290567 GCCAAGGCATGCATCACA 58.709 55.556 21.36 0.00 41.49 3.58
144 214 7.781324 ATTAATTGACCATCACAAGTTTCCT 57.219 32.000 0.00 0.00 0.00 3.36
282 352 8.902540 AGTCGCACCATATATTTGAGATTAAA 57.097 30.769 0.00 0.00 0.00 1.52
283 353 8.902540 AAGTCGCACCATATATTTGAGATTAA 57.097 30.769 0.00 0.00 0.00 1.40
333 403 6.456988 GGTTCTGATTCATTCCAATCACGTAC 60.457 42.308 0.00 0.00 37.77 3.67
362 432 7.527084 AGATATCTTGTTCGTGCTTACTTTC 57.473 36.000 0.00 0.00 0.00 2.62
443 514 8.557029 GTTCGATTTTTATTCGTTATCTCCCAT 58.443 33.333 0.00 0.00 37.82 4.00
467 538 5.014202 AGCCTGGTATGGTTTATTTTCGTT 58.986 37.500 0.00 0.00 0.00 3.85
521 593 3.060272 CACGAATCATCAAGTCCGCATAC 60.060 47.826 0.00 0.00 0.00 2.39
525 597 0.652592 CCACGAATCATCAAGTCCGC 59.347 55.000 0.00 0.00 0.00 5.54
526 598 2.010145 ACCACGAATCATCAAGTCCG 57.990 50.000 0.00 0.00 0.00 4.79
527 599 2.420022 CCAACCACGAATCATCAAGTCC 59.580 50.000 0.00 0.00 0.00 3.85
528 600 3.074412 ACCAACCACGAATCATCAAGTC 58.926 45.455 0.00 0.00 0.00 3.01
529 601 3.140325 ACCAACCACGAATCATCAAGT 57.860 42.857 0.00 0.00 0.00 3.16
531 603 4.457603 CCTTAACCAACCACGAATCATCAA 59.542 41.667 0.00 0.00 0.00 2.57
532 604 4.006989 CCTTAACCAACCACGAATCATCA 58.993 43.478 0.00 0.00 0.00 3.07
533 605 3.181500 GCCTTAACCAACCACGAATCATC 60.181 47.826 0.00 0.00 0.00 2.92
536 608 2.161609 CAGCCTTAACCAACCACGAATC 59.838 50.000 0.00 0.00 0.00 2.52
537 609 2.159382 CAGCCTTAACCAACCACGAAT 58.841 47.619 0.00 0.00 0.00 3.34
538 610 1.141254 TCAGCCTTAACCAACCACGAA 59.859 47.619 0.00 0.00 0.00 3.85
540 612 0.872388 GTCAGCCTTAACCAACCACG 59.128 55.000 0.00 0.00 0.00 4.94
541 613 1.244816 GGTCAGCCTTAACCAACCAC 58.755 55.000 0.00 0.00 35.53 4.16
543 615 3.737702 TGGTCAGCCTTAACCAACC 57.262 52.632 0.00 0.00 42.48 3.77
548 620 3.432326 CCTCCACTATGGTCAGCCTTAAC 60.432 52.174 0.00 0.00 39.03 2.01
551 623 1.207791 CCTCCACTATGGTCAGCCTT 58.792 55.000 0.00 0.00 39.03 4.35
552 624 0.043334 ACCTCCACTATGGTCAGCCT 59.957 55.000 0.00 0.00 39.03 4.58
553 625 2.609046 ACCTCCACTATGGTCAGCC 58.391 57.895 0.00 0.00 39.03 4.85
557 629 0.103208 CTGCGACCTCCACTATGGTC 59.897 60.000 0.00 0.00 46.69 4.02
559 631 1.227380 GCTGCGACCTCCACTATGG 60.227 63.158 0.00 0.00 39.43 2.74
560 632 1.227380 GGCTGCGACCTCCACTATG 60.227 63.158 0.00 0.00 0.00 2.23
561 633 2.786495 CGGCTGCGACCTCCACTAT 61.786 63.158 0.00 0.00 0.00 2.12
564 636 4.681978 AACGGCTGCGACCTCCAC 62.682 66.667 0.00 0.00 0.00 4.02
567 639 4.681978 ACCAACGGCTGCGACCTC 62.682 66.667 0.00 0.00 0.00 3.85
570 642 3.414700 CTCACCAACGGCTGCGAC 61.415 66.667 0.00 0.00 0.00 5.19
572 644 3.958147 ATCCTCACCAACGGCTGCG 62.958 63.158 0.00 0.00 0.00 5.18
573 645 0.392461 TAATCCTCACCAACGGCTGC 60.392 55.000 0.00 0.00 0.00 5.25
574 646 2.332063 ATAATCCTCACCAACGGCTG 57.668 50.000 0.00 0.00 0.00 4.85
575 647 2.421529 GGAATAATCCTCACCAACGGCT 60.422 50.000 0.00 0.00 42.93 5.52
576 648 1.947456 GGAATAATCCTCACCAACGGC 59.053 52.381 0.00 0.00 42.93 5.68
577 649 2.210116 CGGAATAATCCTCACCAACGG 58.790 52.381 0.00 0.00 44.17 4.44
578 650 2.210116 CCGGAATAATCCTCACCAACG 58.790 52.381 0.00 0.00 44.17 4.10
579 651 3.203716 GACCGGAATAATCCTCACCAAC 58.796 50.000 9.46 0.00 44.17 3.77
632 705 9.733556 ACATGTCAAATACACTAGAACCAAATA 57.266 29.630 0.00 0.00 42.09 1.40
673 746 8.257306 GCACTAGAATTTGGGGATTTATGAAAA 58.743 33.333 0.00 0.00 0.00 2.29
691 764 6.945435 TGGGTATTGAGAAAAATGCACTAGAA 59.055 34.615 0.00 0.00 0.00 2.10
753 826 6.663523 CCAACCTTCACCCAACTTTATATCTT 59.336 38.462 0.00 0.00 0.00 2.40
758 831 3.506398 CCCAACCTTCACCCAACTTTAT 58.494 45.455 0.00 0.00 0.00 1.40
760 833 1.691163 CCCCAACCTTCACCCAACTTT 60.691 52.381 0.00 0.00 0.00 2.66
828 904 7.226720 CACATTAGGCCTTATTTGGTACTAGTG 59.773 40.741 12.58 4.59 35.19 2.74
841 917 4.703093 GCCTTTAACACACATTAGGCCTTA 59.297 41.667 12.58 0.11 41.74 2.69
846 922 6.375455 AGAGAATGCCTTTAACACACATTAGG 59.625 38.462 0.00 0.00 31.40 2.69
894 970 2.377810 TGCTCCTGCCATTCCCGAT 61.378 57.895 0.00 0.00 38.71 4.18
935 1011 2.174639 ACCCCACAGATTGTTCAAGTGA 59.825 45.455 0.00 0.00 34.12 3.41
936 1012 2.586425 ACCCCACAGATTGTTCAAGTG 58.414 47.619 0.00 0.00 32.85 3.16
954 1034 3.438781 TGCAATCACTCGGAACAAATACC 59.561 43.478 0.00 0.00 0.00 2.73
964 1044 1.522668 TGGAGTTTGCAATCACTCGG 58.477 50.000 19.92 0.00 40.45 4.63
965 1045 3.058016 ACATTGGAGTTTGCAATCACTCG 60.058 43.478 19.92 11.64 36.23 4.18
966 1046 4.510038 ACATTGGAGTTTGCAATCACTC 57.490 40.909 18.93 18.93 36.23 3.51
968 1048 3.989817 GGAACATTGGAGTTTGCAATCAC 59.010 43.478 10.05 1.70 36.23 3.06
1013 2939 2.376109 CCCTCGCTTGGAGAAGTAGTA 58.624 52.381 0.00 0.00 46.23 1.82
1176 3102 0.179040 GGAGGTGGTTCGTGGTGAAA 60.179 55.000 0.00 0.00 38.60 2.69
1364 3290 1.540267 CAAGAGAGAACTCGTTCGGGA 59.460 52.381 0.00 0.00 46.64 5.14
1467 3393 3.195698 GCATCCACGCCGACCTTC 61.196 66.667 0.00 0.00 0.00 3.46
1611 3537 4.649267 TCCACAACCATTGGAGACATAA 57.351 40.909 10.37 0.00 42.32 1.90
1626 3552 0.105778 TCATCGCGCCATATCCACAA 59.894 50.000 0.00 0.00 0.00 3.33
1651 3577 1.271762 ACACTGTTGCATCAGAGCCAT 60.272 47.619 27.42 5.52 38.63 4.40
1652 3578 0.109153 ACACTGTTGCATCAGAGCCA 59.891 50.000 27.42 0.00 38.63 4.75
1665 3591 1.843376 AGCTGGTAGCCCACACTGT 60.843 57.895 0.00 0.00 43.77 3.55
1735 3661 2.890474 CCGCCGTCCGAAATCCAG 60.890 66.667 0.00 0.00 40.02 3.86
1809 3735 7.657354 CCGGATCTCAAATACATATCAACAAGA 59.343 37.037 0.00 0.00 0.00 3.02
1815 3741 4.532126 AGCCCGGATCTCAAATACATATCA 59.468 41.667 0.73 0.00 0.00 2.15
2088 4014 1.859383 TTGCGACAAGAACATCGTCA 58.141 45.000 0.00 0.00 40.49 4.35
2103 4029 3.000476 GCATGTTGATAACTGCATTTGCG 60.000 43.478 0.00 0.00 45.83 4.85
2196 4122 2.092753 ACCTGCAATCATCTCGTTCCAT 60.093 45.455 0.00 0.00 0.00 3.41
2310 4236 6.453092 AGATTCTTGGAAAGCAGACAAAATG 58.547 36.000 0.00 0.00 45.70 2.32
2311 4237 6.266103 TGAGATTCTTGGAAAGCAGACAAAAT 59.734 34.615 0.00 0.00 45.70 1.82
2327 4253 4.704057 GGTTCCTTGCTTCATGAGATTCTT 59.296 41.667 0.00 0.00 0.00 2.52
2385 4311 1.082756 GAACTGCCGTGAAGCAACG 60.083 57.895 0.16 0.16 43.52 4.10
2425 4351 2.624838 CTGATCCAAACACTGCCTTTGT 59.375 45.455 0.00 0.00 0.00 2.83
2453 4379 1.135859 CCTCAATGACTTTCAGCGCAC 60.136 52.381 11.47 0.00 0.00 5.34
2604 4530 4.524714 GCATTCAGGACTGTAGCTAGGATA 59.475 45.833 0.00 0.00 0.00 2.59
2644 4570 3.621225 TCTGGACTGCCGGATCAG 58.379 61.111 5.05 6.58 44.72 2.90
2736 4662 1.737236 GATATGTCACCGCACTTTGCA 59.263 47.619 0.00 0.00 45.36 4.08
2757 4683 1.072159 AAAAGCACTCTCCGCAGCT 59.928 52.632 0.00 0.00 39.37 4.24
2778 4704 6.459670 TCGGCACTTACTGATGAAATAGTA 57.540 37.500 0.00 0.00 0.00 1.82
3093 5019 3.099141 CCATGGTTGGAAAGGCATTACT 58.901 45.455 2.57 0.00 46.92 2.24
3290 5216 0.617935 TTGATTCTCGGCCATCACCA 59.382 50.000 2.24 0.00 0.00 4.17
3394 5320 1.571460 GTCTTGCTGCAACGGACAG 59.429 57.895 22.41 9.50 38.22 3.51
3552 5647 7.753132 CGGTGTTTGTTATTAGCACATGTTATT 59.247 33.333 0.00 0.00 0.00 1.40
3568 5663 9.804758 TTTTTGAATTAATAGTCGGTGTTTGTT 57.195 25.926 0.00 0.00 0.00 2.83
3643 5749 8.304596 GGAAATTTGCATGATGATGTATCTCAT 58.695 33.333 4.63 0.00 38.57 2.90
3711 5844 0.609957 AGATGGACGTACGTGGACCA 60.610 55.000 28.16 25.87 35.09 4.02
3994 6129 0.035317 CCCAGCAGTGCTTCACTACA 59.965 55.000 16.89 0.00 43.43 2.74
3996 6131 0.035317 CACCCAGCAGTGCTTCACTA 59.965 55.000 16.89 0.00 43.43 2.74
4077 6212 8.768955 GCAGTGACTACAAATATAAATGAGGAG 58.231 37.037 0.00 0.00 0.00 3.69
4078 6213 8.264347 TGCAGTGACTACAAATATAAATGAGGA 58.736 33.333 0.00 0.00 0.00 3.71
4079 6214 8.437360 TGCAGTGACTACAAATATAAATGAGG 57.563 34.615 0.00 0.00 0.00 3.86
4099 6234 0.606401 ACAGCGCAACCTAATGCAGT 60.606 50.000 11.47 0.00 46.76 4.40
4211 6346 5.557576 ACCTAATGATGAAGCTAGATGCA 57.442 39.130 0.00 0.00 45.94 3.96
4286 6421 0.754587 TGCAATGCCACAACCTCACA 60.755 50.000 1.53 0.00 0.00 3.58


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.